I ran Bouguet's calibration toolbox (http://www.vision.caltech.edu/bouguetj/calib_doc/htmls/example.html) on Matlab and have the parameters from the calibration (intrinsic [focal lengths and principal point offsets] and extrinsic [rotation and translations of the checkerboard with respect to the camera]).
Feature coordinate points of the checkerboard on my images are also known.
I want to obtain rectified images so that I can make a disparity map (for which I have the code for) from each pair of rectified images.
How can I go about doing this?
The documentation is here. At the end, it reads "Add these values as constants to your program, call the initUndistortRectifyMap and the remap function to remove distortion and enjoy distortion free inputs with cheap and low quality cameras".
Once your cameras are rectified, you may be interested in the class StereoVar or StereoBM to get the disparity map. Use reprojectImageTo3D once you are done if you want to check that your results look fine in 3D.